1.7.13 Release Notes
Highlight of Features
Frontend Features
LOTS OF TABS!
Community-Contributed Features
Contribution | Contributor | |
SAML Authentication | Kevin Bui | i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. See more information below. |
Ability to specify user parameter defaults | Michael Horvath | This change is meant to allowing user params to take precedence over hive params. Currently, it's the other way around. |
LDAP UPN Support | Michael Horvath Wake Forest | Active Directory enables other methods of binding which are more flexible besides just using the distinguished name. https://docs.microsoft.com/en-us/openspecs/windows_protocols/ms-adts/6a5891b8-928e-4b75-a4a5-0e3b77eaca52. This change is to enable binding the the User Principle Name form, which is very convenient when the distinguished names for users is not easily available (OU by department, etc.). |
API to get all children of an ontology node | Kevin Bui | The metadata GetChildren API call, which returns information on the children of an ontology node, can now be configured to return multiple levels of children (e.g., children, children's children, etc.). This is done by specifying the numLevel parameters. By default, the function assumes numLevel = 1 and will return the direct descendants of the concept, which is one level of children. When the numLevel = -1 the function will return ALL descendants of the concept, otherwise the function will return up to and including the number of levels specified by numLevel (eg. numlevel=2 returns two levels of descendants, numLevel=4 returns four levels of descendants). |
Totalnum Counter Performance Improvements | Darren Henderson University of Kentucky | Performance enhancements on SQL Server totalnum counting to not unnecessarily recompute temp tables. |
Backend Features
SAML Authentication
(LINKS DON'T WORK AND DOCUMENTATION IS INCOMPLETE.)
i2b2 now includes support for SAML-based enterprise authentication via an institutional Identity Provider. To configure this, you need to configure SimpleSAMLPHP (now included with i2b2) to talk to your institution's Identity Provider. To set up SAML:
We will use SimpleSAMLphp for IdP. Place the following files to the folder /etc/shibboleth/:
If you would like to use your own IdP, please visit Configuration - Service Provider 3 - Shibboleth Wiki for advance configurations.
Place the following files in the directory /etc/httpd/conf.d/:
1) Setting up Apache and simplesamlphp: https://simplesamlphp.org/docs/latest/simplesamlphp-install.html
2) Configure the service provider and add an identity provider: https://simplesamlphp.org/docs/latest/simplesamlphp-sp.html
(You will need to generate a cert in /var/www/simplesamlphp/metadata/saml20-idp-remote.php)
Improved Totalnum Scripts
Totalnum Scripts for Postgres and MSSQL have been updated to improve the Totalnum counter performance on very large(>1.5 million) ontology elements such as ACT medications, Debug messages have also been added for troubleshoot purposes
Totalnum Scripts Setup
In the Release_1-7/NewInstall/Metadata/ run the ant script to create the stored procedures. ant -f data_build.xml create_metadata_procedures_release_1-7
Run the stored procedures on your database. This can be done in two ways.
a. Run the ant command to execute the data_build.xml file with below specified target
- POSTGRESQL : ant -f data_build.xml db_metadata_run_total_count_postgresql
- ORACLE : ant -f data_build.xml db_metadata_run_total_count_oracle
- SQL SERVER : ant -f data_build.xml db_metadata_run_total_count_sqlserver
b. Execute the RunTotalNum stored procedure manully against your database in from a sql Client. This can take several hours. Example Usage:
Oracle:
begin
RUNTOTALNUM('observation_fact','i2b2demodata');
end;
Note: If you get the error as: ERROR at line 1: ORA-01031: insufficient privilege, then run the command:
grant create table to (DB USER)
SQL server:
exec RUNTOTALNUM
PostgreSQL:
select RUNTOTALNUM('observation_fact','public')
– (replace 'public' by the schema name for the fact table)
– If using a schema other than public for metadata, you might need to run "set search_path to 'i2b2metadata','public' " first as well
- When finished, verify it is complete by checking that c_totalnum columns in your ontology tables contain numbers (not nulls).
These total counts will be visible in the ontology browser in the web client.
Additional New Stored Procedures
Age In Years Updater
TODO
Concept Dimension Updater
TODO
I2b2-Synthea data Load
A new option is now available for loading Synthea data files into i2b2. Synthetic patient data generated by Synthea is hosted on SyntheticMass..The Synthea sample files have been converted to i2b2-ACT format. The zipped data files can be downloaded from https://github.com/i2b2/i2b2-synthea
Synthea Load Process:
- Create db Schema with name labeled synthea
- Load Synthea data from the sample data files provided
- Download the zipped flat files and extract to them to a local directory
- Using SSMS, import the sample obs file into obvseration_fact table
- Import the sample obs-pat file into patient dimension table.
- Download latest stored procedures from github
- Execute the stored procedures on your database to create the patientnum and encounternumbers
- Download SyntheticMass Data, Version 2 (24 May, 2017)
- Set up an i2b2 project with the ACT ontology.
- Run
create_synthea_table_sqlserver.sql
in your project to create the Synthea tables. - Import the Synthea data you downloaded in step one into the Synthea tables in your project.
- Load the i2b2-to-SNOMED table in this repository into your project. https://www.nlm.nih.gov/healthit/snomedct/us_edition.html
- Run
synthea_to_i2b2_sqlserver.sql
to convert synthea data into i2b2 tables (this will truncate your existing fact and dimension tables!)- Replace references to
i2b2metadata.dbo
in the script. Use the database and schema where your ACT ontology tables are.
- Replace references to
ACT Version-4 Ontology data load
Metadata scripts are now available to load the latest ACT Version-4 Ontology into your i2b2 db schema
ACT4 dataload process:
- Download the newinstall zip package from https://www.i2b2.org/software/download.html?d=452
- Extract the metadata\act folder from the downloaded zip folder
- Replace edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act folder with extracted new act folder
- Edit the db.properties file in your metadata folder to update the project properties to 'ACT'db.project=ACT
- From the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata folder, run the ant command: ant -f data_build.xml db_metadata_load_data
- This will execute the SQL scripts form the edu.harvard.i2b2.data\Release_1-7\NewInstall\Metadata\act folder to create the new ACT4 Ontology tables
- and loads the corresponding metadata.
- You can now verify the new Ontology by logging into the webclient.
The following command will load the corresponding concept_dimension data of the Onbtology tables that will enable you to run queries in the webclient
From a sql Client>select 'insert into concept_dimension select c_dimcode AS concept_path, c_basecode AS concept_cd, c_name AS name_char, null AS concept_blob, update_date AS update_date, download_date as download_date, import_date as import_date, sourcesystem_cd as sourcesystem_cd, 1 as upload_id from '
+c_table_name+' where m_applied_path=''@'' and c_tablename=''CONCEPT_DIMENSION'' and c_columnname=''concept_path'' and c_visualattributes not like ''%I%'' and (c_columndatatype=''T'' or c_columndatatype=''N'') and c_synonym_cd = ''N'' and (m_exclusion_cd is null or m_exclusion_cd='''') and c_basecode is not null and c_basecode!='''''
from <your_dbschema>.dbo.TABLE_ACCESS where c_visualattributes like '%A%'
Improved db Upgrade Process
Currently i2b2 db upgrade is a multi-step process of running upgrade scripts and stored procedures. This release provides a set of upgrade scripts which will perform the complete db upgrade.
based on your current build version.
For example: Following Ant command will upgrade your db instance from 1.7.09c to latest version.
>ant -f data_build.xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12
Steps to Perform db upgrade:
- Backup your existing data folder
- Copy all the folders from the extracted download data folder into your existing data Upgrade folder
Example: Downloads\2b2core-upgrade-1712a\i2b2\data to C:\opt\edu.harvard.i2b2.data\Release_1-7\Upgrade\. This will replace
existing Crcdata, Hivedata, Metadata, PMdata folders.
Alternative to above step, navigate to the edu.harvard.i2b2.data\Release_1-7\Upgrade\ directory of your extracted folder - Copy the db.properties files from your back up into the respective locations(namely Crcdata, Hivedata, Metadata, PMdata )
- Open the command prompt and navigate to cell folders and run the following upgrade ant commands on your i2b2 database instance, where {db} can be Oracle, sqlserver or postgresql.
Alternative to above Step, you can run individual SQL scripts on your db instance in place of ant commands.
In data folder\Release_1-7\Upgrade\ run the ant commands under each individual cell subfolder as below. | |
Upgrade From Build | Upgrade to Latest build |
1.7.09c | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-09c upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-09c upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-09c upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-09c upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.10 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-10 upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-10 upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-10 upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-10 upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.11 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-11 upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-11 upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-11 upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-11 upgrade_pm_tables_release_1-7-12 |
1.7.12 | In the Crcdata folder run the following ant command: ant -f data_build.xml upgrade_table_release_1-7-12 In the Hivedata folder run the following ant command: ant -f data_build.xml upgrade_hive_tables_release_1-7-12 In the Metadata folder run the following ant command: ant -f data_build.xml upgrade_tables_release_1-7-12 In the PMdata folder run the following ant command: ant -f data_build.xml upgrade_pm_tables_release_1-7-12 |
Changelog
Database Drivers
The JDBC drivers were updated to the following versions.
Driver | New Version |
ojdbc8.jar | Oracle 12.2.0.1 |
postgresql-42.2.5.jar | PostgreSQL 42.2.5 |
mssql-jdbc-7.0.0.jre8.jar | MS Sql Server 7.0.0 |
Supported Db Server versions
Type | Version |
SQL Server | 2012+ (tested with up to 2019) |
Oracle | 12g+ and 21c |
Postgres | 9 to 14 |
Supported software versions
Application | Version |
Java | 8 or 11 |
Wildfly | 17.0.0 |
Apache HTD | 2.4.17 or higher |
Apache Ant | 1.9.6 |
Apache Axis2 | 1.7.1 |
PHP | 7.2.27 or higher |
i2b2 Database Changes
New db updates include
- DATA-7 QT_PATIENT_SET_ENC_COLLECTION should be a bigint
- DATA-5 Synthea i2b2 data
- DATA-8 Synthea data load test from Github files
- DATA-6 improve i2b2 db upgrade process
- DATA-12 Stored procedure to update concept dimension
- DATA-11 Age in years updater during demodata install
- DATA-9 ACT v4 ontology
- CORE-389 Totalnum performance improvements
- CORE-394 Obfuscated totalnum reporting tables
- CORE-398 Multifact support for totalnums
- CORE-400 Show totalnums in top level folders
i2b2 Server and Client Changes
New Features and Improvements
- CORE-399 Oracle index hints must use the table alias
- CORE-382 Username / password errors should not specify which had the problem
- WEBCLIENT-334 Provide tabs for major plugins and temporal query
- WEBCLIENT-344 Cleanup Analysis Tools list of Plugins to only Supported Items
- WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name
- WEBCLIENT-320 Provide REFRESH ALL context menu in FindTerms panel
- WEBCLIENT-307 Drag and drop in term info panel
- WEBCLIENT-306 Beth Israel contribution: commas in counts, query option infrastructure
- CORE-402 Fix Veracode identified Security flaws in i2b2 Server-Side Code
- WEBCLIENT-343 Fix Veracode identified Security flaws in i2b2Webclient Code
- CORE-404 Adding support for JDK 11. Now including the gensrc due to jaxb has been removed.
- CORE-413 FetchAllChildren
- CORE-414 SAML
- CORE-415 Log4j upgraded to v2
- CORE-416 User parameter precedence change (contributed by Michael Horvath)
- CORE-417 LDAP UPN support (contributed by Michael Horvath)
- CORE-419 i2b2 - redcap: ability to read from a file instead of from just a redcap api
Bug Fixes
- CORE-418 Local timestamps in sessions on Oracle - appserver /db server in diff time zones
- WEBCLIENT-351 Obfuscated User Not Showing Graph
- WEBCLIENT-342 switch response status check from "OK" to 200 to handle lab value pop up in http/2 protocols
- WEBCLIENT-335 temporal query in webclient with no anchoring events not running
- WEBCLIENT-350 Unable to drag items in workplace
- WEBCLIENT-325 Wayne's improvements to hierarchical find-by-name
- WEBCLIENT-341 Toggle between <and > group panel buttons resulting in blank QueryResults view
- WEBCLIENT-319 FindTerms- exceeding more than 200(default) return count - displaying server error
- WEBCLIENT-316 Admin tool unresponsive in IE11
- WEBCLIENT-305 Occasionally items in Find Terms by name are not draggable
- WEBCLIENT-304 Hierarchical levels in Find Terms might not work in ontologies that have extra backslashes
- WEBCLIENT-294 Webclient Reports "QUERY CANCELLED" While Query Is Still Running
- WEBCLIENT-291 Date constraints popup OK button disabled, maintains new date if canceled
- WEBCLIENT-196 Temporal query more than 2 events is not populating query name in the query name textbox and displaying new event added msg
- WEBCLIENT-156 switching from events grouppanel view to 'same financial encounter' selection is not switching to original concept group panel view
- CORE-282 Error returned when obfuscated user is locked out
- CORE-281 Query continues to run after user receives lockout message
- CORE-412 Disable login to agg service account
- CORE-405 Upgrade JDBC Drivers
- CORE-403 Add result path
- CORE-399 use alias for index hint
Notes for Developers
For Java 11 install, if you change xsd, then modify the gensource.